PDB-5th2: Cetuximab Fab in complex with L5Q meditope variant

ID or keywords:

Entry

Database: PDB / ID: 5th2

Title

Cetuximab Fab in complex with L5Q meditope variant

Components

L5Q meditope
cetuximab Fab, heavy chain
cetuximab Fab, light chain

Keywords

IMMUNE SYSTEM / antibody / anti-EGFR

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 Å

Authors

Bzymek, K.P. / Williams, J.C.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.

History

Deposition	Sep 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Data collection / Derived calculations / Structure summary Category: diffrn_detector / entity / pdbx_struct_oper_list Item: _diffrn_detector.detector / _entity.src_method / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 6, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5th2.cif.gz	374.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5th2.ent.gz	306.8 KB	Display	PDB format
PDBx/mmJSON format	5th2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5th2_validation.pdf.gz	463.5 KB	Display	wwPDB validaton report
Full document	5th2_full_validation.pdf.gz	467.7 KB	Display
Data in XML	5th2_validation.xml.gz	41.8 KB	Display
Data in CIF	5th2_validation.cif.gz	62.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/th/5th2 ftp://data.pdbj.org/pub/pdb/validation_reports/th/5th2	HTTPS FTP

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Related structure data

Related structure data	5etuC 5eukC 5f88C 5ff6C 5i2iC 5iopC 5ir1C 5itfC 5iv2C 5ivzC 5t1kC 5t1lC 5t1mC 4gw1S 4iwe PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2pcp-2 5mub-2 6d9g-1 2uyl-4 4yhn-1 1ce1-d 5vsh-4 1aj7-d 5dqj-1 4jzn-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: cetuximab Fab, light chain

B: cetuximab Fab, heavy chain

C: cetuximab Fab, light chain

D: cetuximab Fab, heavy chain

E: L5Q meditope

F: L5Q meditope

hetero molecules

97.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: cetuximab Fab, light chain

B: cetuximab Fab, heavy chain

E: L5Q meditope

hetero molecules

defined by author&software
48.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: cetuximab Fab, light chain

D: cetuximab Fab, heavy chain

F: L5Q meditope

hetero molecules

defined by author&software
48.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.190, 83.120, 212.560
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	cetuximab Fab, light chain Mass: 23287.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: unidentified (others)
#2: Antibody	cetuximab Fab, heavy chain Mass: 23725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: unidentified (others)
#3: Protein/peptide	L5Q meditope Mass: 1487.727 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citric acid, 0.1 M Na2HPO4, 0.4 M K2HPO4, 1.6 M NaH2PO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.84→44.77 Å / Num. obs: 91890 / % possible obs: 92.3 % / Redundancy: 3.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shell	Resolution: 1.84→1.89 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.787 / CC_1/2: 0.677 / % possible all: 94.6

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1

Resolution: 1.84→44.77 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.32

	R_factor	Num. reflection	% reflection
R_free	0.1844	4594	5 %
R_work	0.1612	-	-
obs	0.1624	91871	92.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.84→44.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6766	0	15	852	7633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7144
X-RAY DIFFRACTION	f_angle_d	0.873	9780
X-RAY DIFFRACTION	f_dihedral_angle_d	12.2	4321
X-RAY DIFFRACTION	f_chiral_restr	0.058	1099
X-RAY DIFFRACTION	f_plane_restr	0.005	1264

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8399-1.8608	0.2846	153	0.2575	2897	X-RAY DIFFRACTION	95
1.8608-1.8827	0.271	156	0.2589	2977	X-RAY DIFFRACTION	94
1.8827-1.9057	0.3119	147	0.2592	2781	X-RAY DIFFRACTION	91
1.9057-1.9298	0.2984	142	0.2556	2704	X-RAY DIFFRACTION	86
1.9298-1.9552	0.2581	156	0.2159	2959	X-RAY DIFFRACTION	95
1.9552-1.982	0.2294	158	0.1935	3014	X-RAY DIFFRACTION	96
1.982-2.0103	0.2151	158	0.1815	2995	X-RAY DIFFRACTION	96
2.0103-2.0403	0.2222	156	0.171	2956	X-RAY DIFFRACTION	96
2.0403-2.0722	0.1987	157	0.1753	2989	X-RAY DIFFRACTION	95
2.0722-2.1061	0.2125	155	0.1694	2943	X-RAY DIFFRACTION	95
2.1061-2.1424	0.219	158	0.1703	3001	X-RAY DIFFRACTION	95
2.1424-2.1814	0.2072	157	0.1764	2974	X-RAY DIFFRACTION	96
2.1814-2.2234	0.2231	156	0.1679	2972	X-RAY DIFFRACTION	95
2.2234-2.2687	0.2376	153	0.1738	2904	X-RAY DIFFRACTION	94
2.2687-2.3181	0.1843	158	0.1672	2999	X-RAY DIFFRACTION	95
2.3181-2.372	0.2045	155	0.1695	2943	X-RAY DIFFRACTION	94
2.372-2.4313	0.2276	141	0.1649	2680	X-RAY DIFFRACTION	86
2.4313-2.497	0.1989	148	0.1597	2816	X-RAY DIFFRACTION	89
2.497-2.5705	0.2128	157	0.1641	2979	X-RAY DIFFRACTION	95
2.5705-2.6535	0.1969	157	0.1611	2983	X-RAY DIFFRACTION	95
2.6535-2.7483	0.1949	156	0.1631	2973	X-RAY DIFFRACTION	94
2.7483-2.8583	0.1749	157	0.1654	2973	X-RAY DIFFRACTION	94
2.8583-2.9884	0.2217	156	0.1663	2969	X-RAY DIFFRACTION	94
2.9884-3.1459	0.1712	153	0.1611	2898	X-RAY DIFFRACTION	92
3.1459-3.3429	0.1678	152	0.1529	2889	X-RAY DIFFRACTION	90
3.3429-3.6009	0.135	138	0.1388	2633	X-RAY DIFFRACTION	82
3.6009-3.9631	0.1619	153	0.1366	2894	X-RAY DIFFRACTION	90
3.9631-4.5361	0.1352	151	0.1238	2882	X-RAY DIFFRACTION	90
4.5361-5.7131	0.1408	152	0.1312	2892	X-RAY DIFFRACTION	89
5.7131-44.7854	0.1768	148	0.1928	2808	X-RAY DIFFRACTION	82

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.9663	1.1875	-1.4511	3.3149	-2.52	5.8442	0.066	-0.0012	0.192	-0.0255	0.1103	0.064	-0.2898	-0.3505	-0.1575	0.2491	0.0746	0.0029	0.222	-0.0082	0.2291	-11.8336	16.9261	-17.8272
2	1.2321	0.1366	0.7257	2.3429	-0.1684	2.3656	0.0741	-0.0884	0.123	0.1047	0.0887	-0.0754	-0.3978	0.1467	-0.155	0.2748	-0.0023	0.0097	0.2307	-0.0275	0.2068	-2.8285	14.1781	-11.9532
3	1.201	-0.4223	-0.3148	2.2582	-1.0581	3.3667	0.0791	-0.0046	0.173	-0.0686	-0.0312	-0.1851	-0.3143	0.2783	-0.0211	0.2455	-0.0005	0.0328	0.2439	-0.0229	0.2103	-2.5353	16.1108	-20.8548
4	1.6131	-0.4824	0.7599	3.3283	-2.0028	2.6469	-0.0201	-0.1199	-0.0761	0.2568	0.1282	0.1654	0.1568	-0.2591	-0.0978	0.2459	0.0147	0.0106	0.2572	-0.0103	0.1977	-9.5917	2.9942	-7.5205
5	0.3714	0.891	-1.7865	2.2157	-4.443	8.9197	0.0629	-0.1129	0.1417	0.4114	0.1259	0.1657	-0.5061	-0.1079	-0.1726	0.2235	0.0209	-0.012	0.1937	-0.0142	0.2239	-6.5805	20.544	-34.2668
6	3.048	-0.2052	0.5904	5.1952	0.0336	2.8541	0.0966	0.506	-0.2218	-0.4879	-0.0064	-0.4433	0.126	0.2941	-0.093	0.1727	-0.0054	0.0047	0.3199	-0.0385	0.2474	2.3966	0.4005	-55.2222
7	0.8852	1.0757	0.8719	5.1715	4.3577	3.86	-0.1704	0.0682	0.1273	-0.0783	0.0163	0.258	-0.0759	-0.1461	0.1806	0.1671	-0.0088	-0.0062	0.2051	0.0383	0.2376	-7.0666	10.1643	-48.9815
8	1.6519	0.4232	1.7661	0.8719	1.0505	2.3203	-0.076	0.1611	0.0606	-0.1478	0.1471	0.1317	-0.2981	0.1723	-0.078	0.2181	-0.0411	-0.0187	0.2796	0.0065	0.2729	-12.1814	4.0028	-54.0776
9	1.3993	0.7153	1.3595	2.6506	1.5084	2.9446	-0.1629	0.1887	0.0971	-0.2552	0.0921	0.1427	-0.2017	0.1114	0.0762	0.1492	-0.0374	0.0081	0.2384	0.0161	0.2324	-5.5571	8.6324	-52.8358
10	2.0001	1.9999	1.9999	2	2	2.0001	3.3963	-9.5896	6.1374	-0.6579	-1.4285	-2.2762	-3.6389	5.7229	-1.9941	0.7061	-0.2576	0.323	0.849	-0.1508	0.9634	4.3843	4.689	-67.1068
11	3.4457	1.1287	2.9089	3.1353	3.5268	6.4041	-0.0634	0.4874	-0.1224	0.1892	0.292	-0.0046	0.5321	0.3386	-0.207	0.3188	0.0358	0.0141	0.2052	-0.0055	0.264	2.7226	-10.5483	-23.0178
12	1.027	0.4396	0.184	1.3676	0.3436	3.7055	-0.0149	-0.1207	-0.1167	0.068	0.0748	-0.0756	0.3853	0.0943	-0.0656	0.2759	0.0359	-0.0108	0.2159	-0.0158	0.2267	0.8153	-6.5977	-12.7651
13	1.8748	1.1578	-0.8249	3.3658	-0.7056	1.7806	-0.0103	0.0166	0.0502	-0.0339	-0.0146	-0.0533	0.0956	0.1134	0.0218	0.1418	0.0022	-0.0144	0.2168	-0.0168	0.2111	6.6329	0.0134	-43.9456
14	2.9801	2.2722	1.408	5.1362	3.3883	5.4694	0.1371	-0.1103	-0.0596	0.1449	0.0293	-0.3323	0.3706	0.2057	-0.149	0.2394	0.0769	-0.0413	0.1992	-0.0046	0.2365	-19.1548	23.6437	-19.3566
15	1.3935	0.0715	-0.6671	2.2351	0.745	2.4441	0.0414	-0.075	-0.0329	0.314	0.0457	-0.0485	0.2791	0.0086	-0.0926	0.2566	0.0092	-0.0196	0.196	0.011	0.1949	-28.1712	26.5025	-13.4266
16	1.3657	0.0253	-0.0213	3.0615	1.9691	2.9704	0.1281	-0.1137	-0.0854	0.1863	0.0736	-0.2603	0.1788	-0.0328	-0.2303	0.2058	0.0261	-0.0432	0.2321	0.0225	0.1989	-25.3818	29.9462	-16.9562
17	0.4307	0.8764	2.0287	1.9753	4.3721	9.7379	0.0804	-0.0723	-0.1286	0.3244	0.1715	-0.1874	0.321	-0.0095	-0.2915	0.259	0.0233	-0.0209	0.1869	0.0132	0.2289	-24.7405	18.3262	-35.3758
18	1.5309	-0.2676	-0.3118	3.0917	-1.4955	3.646	-0.0166	0.0947	0.0299	-0.0134	0.0765	0.0183	-0.23	-0.0335	-0.0415	0.1674	-0.021	-0.0095	0.205	0.0253	0.2139	-28.7717	31.0606	-53.9038
19	1.5378	0.5295	-1.7063	0.635	-1.0351	2.3762	0.0173	0.0019	-0.0441	-0.0579	-0.0156	-0.1534	0.2069	0.1254	0.0015	0.2062	-0.011	0.0249	0.243	0.0217	0.2638	-19.7697	33.399	-56.4247
20	1.8687	-1.0306	-0.7981	3.0094	-1.0435	3.1439	0.1814	0.2004	0.1589	-0.1349	-0.1329	-0.2034	-0.2723	0.0932	-0.0321	0.148	-0.0218	-0.0031	0.2291	0.0359	0.2014	-26.6166	30.7449	-53.5689
21	3.7816	-2.262	1.6048	4.0918	-5.4376	8.1967	0.0201	0.5162	-0.1935	-0.6084	-0	0.1366	0.4497	-0.2528	-0.1438	0.3242	-0.0404	-0.0687	0.3283	-0.0159	0.2904	-26.6386	23.0215	-60.0353
22	1.0383	0.2692	-0.2147	1.7502	-0.4935	3.5505	0.0241	-0.0575	0.1375	0.0446	0.0688	0.0664	-0.4206	-0.093	-0.09	0.2236	0.0112	0.0106	0.1903	0.005	0.198	-33.0954	47.1823	-17.3579
23	2.1799	1.6273	0.4787	3.7627	0.7672	2.2135	-0.0251	0.0117	-0.0707	-0.0434	-0.0564	0.059	-0.0879	-0.0388	0.0833	0.1297	0.0124	0.0018	0.1863	0.0221	0.2218	-38.7398	36.7457	-46.9568
24	7.8859	-1.6725	0.033	9.656	-0.2396	7.4016	0.4031	0.6915	-0.5325	-0.9383	-0.2226	0.7035	-0.0974	-0.5209	-0.1794	0.3236	0.0705	-0.0544	0.3069	-0.0733	0.2519	-8.1037	4.1636	-28.4372
25	9.649	0.2309	0.7571	9.2739	-0.6215	8.4905	0.2759	0.5291	0.3804	-0.9167	-0.0953	-0.6989	-0.1091	0.5504	-0.1859	0.2869	0.0395	0.0365	0.2864	0.0321	0.2306	-23.4932	35.0689	-30.8944

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 90 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 91 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 113 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 114 through 128 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 129 through 150 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 151 through 163 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 164 through 212 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 213 through 213 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 16 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 17 through 117 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 118 through 221 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 25 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 26 through 75 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 76 through 101 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 102 through 113 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 114 through 150 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 151 through 163 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 164 through 198 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 199 through 213 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1 through 117 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 118 through 220 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1 through 12 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 1 through 12 )

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About Yorodumi

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Yorodumi